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Lim J, Zhou S, Baek J, Kim AY, Valera E, Sweedler J, Bashir R. A Blood Drying Process for DNA Amplification. Small 2024; 20:e2307959. [PMID: 37888793 DOI: 10.1002/smll.202307959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 10/28/2023]
Abstract
The presence of numerous inhibitors in blood makes their use in nucleic acid amplification techniques difficult. Current methods for extracting and purifying pathogenic DNA from blood involve removal of inhibitors, resulting in low and inconsistent DNA recovery rates. To address this issue, a biphasic method is developed that simultaneously achieves inhibitor inactivation and DNA amplification without the need for a purification step. Inhibitors are physically trapped in the solid-phase dried blood matrix by blood drying, while amplification reagents can move into the solid nano-porous dried blood and initiate the amplification. It is demonstrated that the biphasic method has significant improvement in detection limits for bacteria such as Escherichia coli, Methicillin-resistant Staphylococcus aureus, Methicillin-Sensitive Staphylococcus aureus using loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA). Several factors, such as drying time, sample volume, and material properties are characterized to increase sensitivity and expand the application of the biphasic assay to blood diagnostics. With further automation, this biphasic technique has the potential to be used as a diagnostic platform for the detection of pathogens eliminating lengthy culture steps.
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Affiliation(s)
- Jongwon Lim
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuaizhen Zhou
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Janice Baek
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alicia Yeaeun Kim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jonathan Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biomedical and Translational Science, Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Kawaguchi M, Aoki H, Kamo H, Miura K, Hiruta Y, Simizu S, Citterio D. Simplified capture, extraction, and amplification of cellular DNA from water samples. ANAL SCI 2024; 40:501-510. [PMID: 38142247 DOI: 10.1007/s44211-023-00482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/27/2023] [Indexed: 12/25/2023]
Abstract
DNA analysis in water samples is attracting attention in various fields. However, conventional methods for DNA analysis require a work-intensive and time-consuming sample pre-treatment. In this study, a simplified pre-treatment method for analyzing DNA in water samples was evaluated. The process consists of filtration, DNA extraction, and amplification, which can be achieved within a short time. In the filtration process, two types of filters, firstly a tissue paper (Kimwipe) and then a glass filter (GF/F), were used in sequence. The first large pore size filter enabled a reduction in filtration time by removing large particulate matter impurities present in river water matrix. Cells spiked into 1 L of river water were recovered at more than 90% within approximately 5 min filtration time. Also, DNA was extracted from the captured cells directly on the surface of the filter in only 5 min. Thus, DNA collection and extraction from a water sample can be completed within about 10 min. Furthermore, PCR amplification was performed directly from DNA-attached filter sections, which greatly reduced the number of required pre-treatment steps. Finally, we succeeded in establishing a simple and fast on-site pre-treatment system by using a hand-driven syringe filtration method. This pre-treatment system is expected to offer the possibility for the future establishment of a rapid and easy DNA analysis method applicable to various types of water samples.
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Affiliation(s)
- Mai Kawaguchi
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Hiroshi Aoki
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Hiroki Kamo
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Kazuki Miura
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Yuki Hiruta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan.
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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Wan Y, Mu Q, Krzysztoń R, Cohen J, Coraci D, Helenek C, Tompkins C, Lin A, Farquhar K, Cross E, Wang J, Balázsi G. Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance. Proc Natl Acad Sci U S A 2023; 120:e2303114120. [PMID: 38019857 DOI: 10.1073/pnas.2303114120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Drug resistance continues to impede the success of cancer treatments, creating a need for experimental model systems that are broad, yet simple, to allow the identification of mechanisms and novel countermeasures applicable to many cancer types. To address these needs, we investigated a set of engineered mammalian cell lines with synthetic gene circuits integrated into their genome that evolved resistance to Puromycin. We identified DNA amplification as the mechanism underlying drug resistance in 4 out of 6 replicate populations. Triplex-forming oligonucleotide (TFO) treatment combined with Puromycin could efficiently suppress the growth of cell populations with DNA amplification. Similar observations in human cancer cell lines suggest that TFOs could be broadly applicable to mitigate drug resistance, one of the major difficulties in treating cancer.
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Affiliation(s)
- Yiming Wan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Rafał Krzysztoń
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Joseph Cohen
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Damiano Coraci
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Christopher Helenek
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Annie Lin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Kevin Farquhar
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794
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5
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Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. Small Methods 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
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Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
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6
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Gray ZH, Chakraborty D, Duttweiler RR, Alekbaeva GD, Murphy SE, Chetal K, Ji F, Ferman BI, Honer MA, Wang Z, Myers C, Sun R, Kaniskan HÜ, Toma MM, Bondarenko EA, Santoro JN, Miranda C, Dillingham ME, Tang R, Gozani O, Jin J, Skorski T, Duy C, Lee H, Sadreyev RI, Whetstine JR. Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement. Cell 2023; 186:4528-4545.e18. [PMID: 37788669 PMCID: PMC10591855 DOI: 10.1016/j.cell.2023.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/01/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.
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Affiliation(s)
- Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Reuben R Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Gulnaz D Alekbaeva
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sedona E Murphy
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Myers
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Renhong Sun
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Monika Maria Toma
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - John N Santoro
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Christopher Miranda
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Megan E Dillingham
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA; School of Life Science and Technology, Harbin Institute of Technology, 150000 Harbin, China
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomasz Skorski
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Fels Cancer Institute for Personalized Medicine, Temple University School of Medicine, 3420 N. Broad Street, MRB 548, Philadelphia, PA 19140, USA
| | - Cihangir Duy
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA.
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Burkin KM, Ivanov AV, Zherdev AV, Dzantiev BB, Safenkova IV. A Critical Study on DNA Probes Attached to Microplate for CRISPR/Cas12 Trans-Cleavage Activity. Biosensors (Basel) 2023; 13:824. [PMID: 37622910 PMCID: PMC10452489 DOI: 10.3390/bios13080824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
CRISPR/Cas12-based biosensors are emerging tools for diagnostics. However, their application of heterogeneous formats needs the efficient detection of Cas12 activity. We investigated DNA probes attached to the microplate surface and cleaved by Cas12a. Single-stranded (ss) DNA probes (19 variants) and combined probes with double-stranded (ds) and ssDNA parts (eight variants) were compared. The cleavage efficiency of dsDNA-probes demonstrated a bell-shaped dependence on their length, with a cleavage maximum of 50%. On the other hand, the cleavage efficiency of ssDNA probes increased monotonously, reaching 70%. The most effective ssDNA probes were integrated with fluorescein, antibodies, and peroxidase conjugates as reporters for fluorescent, lateral flow, and chemiluminescent detection. Long ssDNA probes (120-145 nt) proved the best for detecting Cas12a trans-activity for all of the tested variants. We proposed a test system for the detection of the nucleocapsid (N) gene of SARS-CoV-2 based on Cas12 and the ssDNA-probe attached to the microplate surface; its fluorescent limit of detection was 0.86 nM. Being united with pre-amplification using recombinase polymerase, the system reached a detection limit of 0.01 fM, thus confirming the effectiveness of the chosen ssDNA probe for Cas12-based biosensors.
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Affiliation(s)
| | | | | | | | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (K.M.B.); (A.V.I.); (A.V.Z.); (B.B.D.)
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8
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Ivanov AV, Safenkova IV, Zherdev AV, Wan Y, Dzantiev BB. Comparison of Single-Stranded DNA Probes Conjugated with Magnetic Particles for Trans-Cleavage in Cas12a-Based Biosensors. Biosensors (Basel) 2023; 13:700. [PMID: 37504099 PMCID: PMC10376970 DOI: 10.3390/bios13070700] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Biosensors based on endonuclease Cas12 provide high specificity in pathogen detection. Sensitive detection using Cas12-based assays can be achieved using trans-cleaved DNA probes attached to simply separated carriers, such as magnetic particles (MPs). The aim of this work was to compare polyA, polyC, and polyT single-stranded (ss) DNA with different lengths (from 10 to 145 nt) as trans-target probes were immobilized on streptavidin-covered MPs. Each ssDNA probe was labeled using fluorescein (5') and biotin (3'). To compare the probes, we used guide RNAs that were programmed for the recognition of two bacterial pathogens: Dickeya solani (causing blackleg and soft rot) and Erwinia amylovora (causing fire blight). The Cas12 was activated by targeting double-stranded DNA fragments of D. solani or E. amylovora and cleaved the MP-ssDNA conjugates. The considered probes demonstrated basically different dependencies in terms of cleavage efficiency. PolyC was the most effective probe when compared to polyA or polyT probes of the same length. The minimal acceptable length for the cleavage follows the row: polyC < polyT < polyA. The efficiencies of polyC and polyT probes with optimal length were proven for the DNA targets' detection of D. solani and E. amylovora. The regularities found can be used in Cas12a-based detection of viruses, bacteria, and other DNA/RNA-containing analytes.
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Affiliation(s)
- Aleksandr V Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Marine College, Hainan University, Haikou 570228, China
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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9
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Zwolinska K, Bienkowska-Haba M, Scott RS, Keiffer T, Sapp M. Experimental Support for Human Papillomavirus Genome Amplification Early after Infectious Delivery. J Virol 2023; 97:e0021423. [PMID: 37223953 PMCID: PMC10308938 DOI: 10.1128/jvi.00214-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/01/2023] [Indexed: 05/25/2023] Open
Abstract
Even though replication and transcription of human papillomavirus type 16 (HPV16) has been intensively studied, little is known about immediate-early events of the viral life cycle due to the lack of an efficient infection model allowing genetic dissection of viral factors. We employed the recently developed infection model (Bienkowska-Haba M, Luszczek W, Myers JE, Keiffer TR, et al. 2018. PLoS Pathog 14:e1006846) to investigate genome amplification and transcription immediately after infectious delivery of viral genome to nuclei of primary keratinocytes. Using 5-ethynyl-2'-deoxyuridine (EdU) pulse-labeling and highly sensitive fluorescence in situ hybridization, we observed that the HPV16 genome is replicated and amplified in an E1- and E2-dependent manner. Knockout of E1 resulted in failure of the viral genome to replicate and amplify. In contrast, knockout of the E8^E2 repressor led to increased viral genome copy number, confirming previous reports. Genome copy control by E8^E2 was confirmed for differentiation-induced genome amplification. Lack of functional E1 had no effect on transcription from the early promoter, suggesting that viral genome replication is not required for p97 promoter activity. However, infection with an HPV16 mutant virus defective for E2 transcriptional function revealed a requirement of E2 for efficient transcription from the early promoter. In the absence of the E8^E2 protein, early transcript levels are unaltered and even decreased when normalized to genome copy number. Surprisingly, a lack of functional E8^E2 repressor did not affect E8^E2 transcript levels when normalized to genome copy number. These data suggest that the main function of E8^E2 in the viral life cycle is to control genome copy number. IMPORTANCE It is being assumed that human papillomavirus (HPV) utilizes three different modes of replication during its life cycle: initial amplification during the establishment phase, genome maintenance, and differentiation-induced amplification. However, HPV16 initial amplification was never formally proven due to a lack of an infection model. Using our recently established infection model (Bienkowska-Haba M, Luszczek W, Myers JE, Keiffer TR, et al. 2018. PLoS Pathog 14:e1006846), we demonstrate herein that viral genome is indeed amplified in an E1- and E2-dependent manner. Furthermore, we find that the main function of the viral repressor E8^E2 is to control viral genome copy number. We did not find evidence that it regulates its own promoter in a negative feedback loop. Our data also suggest that the E2 transactivator function is required for stimulation of early promoter activity, which has been debated in the literature. Overall, this report confirms the usefulness of the infection model for studying early events of the HPV life cycle using mutational approaches.
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Affiliation(s)
- Katarzyna Zwolinska
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA
| | - Malgorzata Bienkowska-Haba
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA
| | - Rona S. Scott
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA
| | - Timothy Keiffer
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA
| | - Martin Sapp
- Department of Microbiology and Immunology, Center for Molecular and Tumor Virology, Feist Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA
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10
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Abstract
In cell-free gene expression, low input DNA concentration severely limits the phenotypic output, which may impair in vitro protein evolution efforts. We address this challenge by developing CADGE, a strategy that is based on clonal isothermal amplification of a linear gene-encoding dsDNA template by the minimal Φ29 replication machinery and in situ transcription-translation. We demonstrate the utility of CADGE in bulk and in clonal liposome microcompartments to boost up the phenotypic output of soluble and membrane-associated proteins, as well as to facilitate the recovery of encapsulated DNA. Moreover, we report that CADGE enables the enrichment of a DNA variant from a mock gene library via either a positive feedback loop-based selection or high-throughput screening. This new biological tool can be implemented for cell-free protein engineering and the construction of a synthetic cell.
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Affiliation(s)
- Zhanar Abil
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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11
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Ivanov AV, Safenkova IV, Biketov SF, Zherdev AV, Dzantiev BB. Engineering of DNA Structures Attached to Magnetic Particles for Effective Trans- and Cis-Cleavage in Cas12-Based Biosensors. Int J Mol Sci 2023; 24:ijms24054484. [PMID: 36901914 PMCID: PMC10003267 DOI: 10.3390/ijms24054484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Sequence-specific endonuclease Cas12-based biosensors have rapidly evolved as a strong tool to detect nucleic acids. Magnetic particles (MPs) with attached DNA structures could be used as a universal platform to manipulate the DNA-cleavage activity of Cas12. Here, we propose nanostructures of trans- and cis-DNA targets immobilized on the MPs. The main advantage of the nanostructures is a rigid double-stranded DNA adaptor that distances the cleavage site from the MP surface to ensure maximum Cas12 activity. Adaptors with different lengths were compared by detecting the cleavage by fluorescence and gel electrophoresis of the released DNA fragments. The length-dependent effects for cleavage on the MPs' surface were found both for cis- and trans-targets. For trans-DNA targets with a cleavable 15-dT tail, the results showed that the optimal range of the adaptor length was 120-300 bp. For cis-targets, we varied the length and location of the adaptor (at the PAM or spacer ends) to estimate the effect of the MP's surface on the PAM-recognition process or R-loop formation. The sequential arrangement of an adaptor, PAM, and a spacer was preferred and required the minimum adaptor length of 3 bp. Thus, with cis-cleavage, the cleavage site can be located closer to the surface of the MPs than with trans-cleavage. The findings provide solutions for efficient Cas12-based biosensors using surface-attached DNA structures.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
- Correspondence: ; Tel./Fax: +7-495-954-2804
| | - Sergey F. Biketov
- State Research Center for Applied Microbiology & Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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12
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McCaughan C, Lenz KA. DNA Amplification Using Promega's PowerPlex ® Fusion Systems (5C and 6C). Methods Mol Biol 2023; 2685:207-226. [PMID: 37439984 DOI: 10.1007/978-1-0716-3295-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Multiplex amplification and typing of short tandem repeat (STR) loci enable the rapid characterization of forensic samples for human identification purposes with the potential for high discriminatory power. Many commercial multiplex kits are available for consideration and purchase by DNA testing laboratories, including the PowerPlex® Fusion 5C and PowerPlex® Fusion 6C Systems offered by Promega Corporation. Herein we describe full-volume and half-volume amplification protocols utilizing extracted DNA for these respective multiplex kits, as well as procedures for direct amplification of lytic and nonlytic storage card punches and swabs.
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13
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Merenciano M, Coronado-Zamora M, González J. Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR). Methods Mol Biol 2023; 2607:95-114. [PMID: 36449160 DOI: 10.1007/978-1-0716-2883-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs), also known as transposons, are repetitive DNA sequences, present in virtually all organisms, that can move from one genomic position to another. TEs can be a source of mutations with important consequences for organisms. Despite their interest, its repetitive nature has made their study very challenging. However, the emergence of new sequencing technologies that allow obtaining long-read sequences, has improved the in silico de novo detection and annotation of TEs. The de novo annotation of TEs has already been performed in several organisms including the fruit fly Drosophila melanogaster. Yet, experimental validation can be used to confirm the presence of TEs in specific D. melanogaster natural populations. Here, we present a step-by-step protocol to experimentally validate by polymerase chain reaction (PCR) the presence and/or absence of TEs in natural populations of D. melanogaster. This detailed protocol has been implemented in the participant high schools of the Citizen Fly Lab activity that is part of the international citizen science project Melanogaster: Catch the Fly! ( https://melanogaster.eu ). Specifically, the students collaborate with the scientists of the European Drosophila Population Genomics Consortium (DrosEU) in the experimental validation of new genetic variants, previously identified using bioinformatic techniques.
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Affiliation(s)
| | | | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona, Spain.
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14
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Qiao H, Gao Y, Liu Q, Wei Y, Li J, Wang Z, Qi H. Oligo replication advantage driven by GC content and Gibbs free energy. Biotechnol Lett 2022. [PMID: 36029395 DOI: 10.1007/s10529-022-03295-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/25/2022] [Indexed: 11/02/2022]
Abstract
Large scale DNA oligo pools are emerging as a novel material in a variety of advanced applications. However, GC content and length cause significant bias in amplification of oligos. We systematically explored the amplification of one oligo pool comprising of over ten thousand distinct strands with moderate GC content in the range of 35-65%. Uniqual amplification of oligos result to the increased Gini index of the oligo distribution while a few oligos greatly increased their proportion after 60 cycles of PCR. However, the significantly enriched oligos all have relatively high GC content. Further thermodynamic analysis demonstrated that a high value of both GC content and Gibbs free energy could improve the replication of specific oligos during biased amplification. Therefore, this double-G (GC content and Gibbs free energy) driven replication advantage can be used as a guiding principle for the sequence design for a variety of applications, particularly for data storage.
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15
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Matsuura SI, Baba T, Ikeda T, Yamamoto K, Tsunoda T, Yamaguchi A. Highly Precise and Sensitive Polymerase Chain Reaction Using Mesoporous Silica-Immobilized Enzymes. ACS Appl Mater Interfaces 2022; 14:29483-29490. [PMID: 35700238 PMCID: PMC9266630 DOI: 10.1021/acsami.2c01992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A highly precise and sensitive technology that enables DNA amplification/detection from minimal amounts of nucleic acid is expected to find applicability in genetic testing involving small amounts of samples. The use of a free enzyme in conventional DNA amplification techniques, such as the polymerase chain reaction (PCR), frequently causes side reactions (i.e., nonspecific DNA amplification) when ≤103 substrate DNA molecules are present, thereby preventing selective amplification of the target DNA. To address this issue, we have developed a novel DNA amplification system, mesoporous silica-enhanced PCR (MSE-PCR), which involves the immobilization of a thermostable DNA polymerase from Thermococcus kodakaraensis (KOD DNA polymerase) into highly ordered nanopores of the mesoporous silica to control the reaction environment around the enzyme. In the MSE-PCR system using immobilized KOD DNA polymerase, such nonspecific DNA amplification was remarkably inhibited under the same conditions. Furthermore, the optimization of mesoporous silica pore sizes enabled selective and efficient DNA amplification from DNA substrates at the single-molecule level, i.e., one ten-thousandth of the amount of substrate DNA required for a DNA amplification reaction using a free enzyme. The results obtained in this study have shown that the nanopores of mesoporous silica can inhibit nonspecific reactions in DNA amplification, thereby considerably improving the specificity and sensitivity of the DNA polymerase reaction.
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Affiliation(s)
- Shun-ichi Matsuura
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Tomoya Baba
- Advanced
Genomics Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Joint
Support-Center for Data Science Research, Research Organization of Information and Systems, 10-3 Midori-cho, Tachikawa, Tokyo 190-0014, Japan
| | - Takuji Ikeda
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Katsutoshi Yamamoto
- Faculty
of Environmental Engineering, The University
of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka 808-0135, Japan
| | - Tatsuo Tsunoda
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
| | - Aritomo Yamaguchi
- Research
Institute for Chemical Process Technology, National Institute of Advanced Industrial Science and Technology
(AIST), 4-2-1 Nigatake, Miyagino-ku, Sendai, Miyagi 983-8551, Japan
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16
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Agustriana E, Nuryana I, Laksmi FA, Dewi KS, Wijaya H, Rahmani N, Yudiargo DR, Ismadara A, Helbert, Hadi MI, Purnawan A, Cameliawati Djohan A. Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system. Prep Biochem Biotechnol 2022; 53:384-393. [PMID: 35792906 DOI: 10.1080/10826068.2022.2095573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Bst DNA polymerase is a DNA polymerase derived from Geobacillus stearothermophilus, has a strand-displacement activity, and is used in loop-mediated isothermal amplification (LAMP) for rapid detection of COVID-19. Despite its potential to be employed in the detection of COVID-19, using commercially available enzymes is not economically feasible. The use of noncommercial enzyme for routine use is desirable. However, research on Bst DNA polymerase is still limited in Indonesia. For those reasons, a preliminary study of scale-up production of recombinant Bst polymerase was conducted. Therefore, the optimization of expression conditions was performed. The optimum conditions for Bst polymerase expression were as follows: 1 mM of IPTG, post-induction incubation time of 6 h, and induction at OD600 1.1. Employing optimum conditions could result in 2.8 times increase in protein yield compared to the initial conditions. Subsequently, an operation in 1 L working volume by a lab-scale bioreactor had been performed, followed by purification and dialysis. The optimum result for a 1 L lab-scale bioreactor was achieved by applying 100 rpm and 3 vvm, giving 11.7 mg/L of protein yield. Bst polymerase was successfully purified showing 813.56 U/mg of polymerase activity.
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Affiliation(s)
- Eva Agustriana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Hans Wijaya
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Nanik Rahmani
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Danu Risqi Yudiargo
- Biology Department, Institut Teknologi Sepuluh Nopember, Surabaya, Indonesia
| | | | - Helbert
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Moch Irfan Hadi
- Department of Biology, Sunan Ampel State Islamic University, Surabaya, Indonesia
| | - Awan Purnawan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Apridah Cameliawati Djohan
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Bogor, Indonesia
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17
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Hamrun N, Ruslin M, Marlina E, Oktawati S, Saito T, Yusuf ASH, Ou KL. Profile of vitamin D receptor gene polymorphism TaqI in patients with periodontitis. Biomed Rep 2022; 16:35. [PMID: 35386105 PMCID: PMC8972835 DOI: 10.3892/br.2022.1518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/11/2022] [Indexed: 01/09/2023] Open
Abstract
The present study aimed to assess the incidence of the vitamin D receptor (VDR) gene polymorphism TaqI in patients with periodontitis, and the potential association of this polymorphism with the severity of the disease. This was a case-controlled study, which included 162 adults divided into two groups as follows: Case group (81 patients diagnosed with periodontitis) and control group (81 patients without periodontitis). Venous blood was obtained from each sample from which DNA was extracted. The gene polymorphism was determined using restricted fragment length polymorphism-PCR and DNA sequencing to identify endonuclease restrictions in exon 9 (TaqI). The data were analyzed using an independent samples t-test. VDR gene polymorphisms were detected in periodontitis cases with TT (86.4%), Tt (12.4%) and tt (1.2%) genotypes. DNA sequencing confirmed a change in the sequence of the VDR gene nucleotides in patients with periodontitis. The data indicated that the severity of periodontal tissue damage may be influenced by changes in the nucleotide sequence.
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Affiliation(s)
- Nurlindah Hamrun
- Department of Oral Biology, Faculty of Dentistry, Hasanuddin University, Makassar, South Sulawesi 90425, Indonesia,Correspondence to: Dr Nurlindah Hamrun, Department of Oral Biology, Faculty of Dentistry, Hasanuddin University, Jl. Perintis Kemerdekaan KM 10, Makassar, South Sulawesi 90425, Indonesia
| | - Muhammad Ruslin
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Hasanuddin University, Makassar, South Sulawesi 90425, Indonesia
| | - Erni Marlina
- Department of Oral Medicine, Faculty of Dentistry, Hasanuddin University, Makassar, South Sulawesi 90425, Indonesia
| | - Sri Oktawati
- Department of Periodontology, Faculty of Dentistry, Hasanuddin University, Makassar, South Sulawesi 90425, Indonesia
| | - Takashi Saito
- Division of Clinical Cariology and Endodontology, Department of Oral Rehabilitation, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido 060-8586, Japan
| | - Andi Sitti Hajrah Yusuf
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Hasanuddin University, Makassar, South Sulawesi 90425, Indonesia
| | - Keng-Liang Ou
- Department of Dentistry, Taipei Medical University-Shuang Ho Hospital, New Taipei City 235, Taiwan, R.O.C,Biomedical Technology R&D Center, China Medical University Hospital, Taichung 404, Taiwan, R.O.C
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18
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Georgoutsou-Spyridonos M, Filippidou M, Kaprou GD, Mastellos DC, Chatzandroulis S, Tserepi A. Isothermal Recombinase Polymerase Amplification (RPA) of E. coli gDNA in Commercially Fabricated PCB-Based Microfluidic Platforms. Micromachines (Basel) 2021; 12:1387. [PMID: 34832799 DOI: 10.3390/mi12111387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/04/2021] [Accepted: 11/10/2021] [Indexed: 12/04/2022]
Abstract
Printed circuit board (PCB) technology has been recently proposed as a convenient platform for seamlessly integrating electronics and microfluidics in the same substrate, thus facilitating the introduction of integrated and low-cost microfluidic devices to the market, thanks to the inherent upscaling potential of the PCB industry. Herein, a microfluidic chip, encompassing on PCB both a meandering microchannel and microheaters to accommodate recombinase polymerase amplification (RPA), is designed and commercially fabricated for the first time on PCB. The developed microchip is validated for RPA-based amplification of two E. coli target genes compared to a conventional thermocycler. The RPA performance of the PCB microchip was found to be well-comparable to that of a thermocycler yet with a remarkably lower power consumption (0.6 W). This microchip is intended for seamless integration with biosensors in the same PCB substrate for the development of a point-of-care (POC) molecular diagnostics platform.
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Basmaciyan L, François A, Vincent A, Valot S, Bonnin A, Costa D, Razakandrainibe R, Morio F, Favennec L, Dalle F. Commercial Simplex and Multiplex PCR Assays for the Detection of Intestinal Parasites Giardia intestinalis, Entamoeba spp., and Cryptosporidium spp.: Comparative Evaluation of Seven Commercial PCR Kits with Routine In-House Simplex PCR Assays. Microorganisms 2021; 9:2325. [PMID: 34835453 DOI: 10.3390/microorganisms9112325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 02/04/2023] Open
Abstract
Nowadays, many commercial kits allowing the detection of digestive parasites by DNA amplification methods have been developed, including simplex PCR assays (SimpPCRa) allowing the identification of a single parasite, and multiplex PCR assays (MultPCRa) allowing the identification of several parasites at once. Thus, aimed at improving the diagnosis of intestinal protozoal infections, it is essential to evaluate the performances of these new tools. A total of 174 DNA samples collected between 2007 and 2017 were retrospectively included in this study. Performances of four commercial SimpPCRa (i.e., CerTest-VIASURETM) and three MultPCRa (i.e., CerTest-VIASURETM, FAST-TRACK-Diagnostics-FTD-Stool-ParasiteTM and DIAGENODE-Gastroenteritis/Parasite-panel-ITM) were evaluated for the detection of Cryptosporidium spp., Entamoeba spp., and Giardia intestinalis in stool samples compared to our routinely used in-house SimpPCRa. Globally, the SimpPCRa showed better sensitivity/specificity for the detection of G. intestinalis, E. histolytica, E. dispar, and Cryptosporidium spp. (i.e., 96.9/93.6%; 100/100%; 95.5/100%; and 100/99.3%, respectively), compared to the three commercial MultPCRa tested. All in all, we showed that MultPCRa offer an interesting alternative for the detection of protozoans in stool samples depending on the clinical context.
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20
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Zimmers ZA, Boyd AD, Stepp HE, Adams NM, Haselton FR. Development of an Automated, Non-Enzymatic Nucleic Acid Amplification Test. Micromachines (Basel) 2021; 12:1204. [PMID: 34683255 DOI: 10.3390/mi12101204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/23/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022]
Abstract
Among nucleic acid diagnostic strategies, non-enzymatic tests are the most promising for application at the point of care in low-resource settings. They remain relatively under-utilized, however, due to inadequate sensitivity. Inspired by a recent demonstration of a highly-sensitive dumbbell DNA amplification strategy, we developed an automated, self-contained assay for detection of target DNA. In this new diagnostic platform, called the automated Pi-powered looping oligonucleotide transporter, magnetic beads capture the target DNA and are then loaded into a microfluidic reaction cassette along with the other reaction solutions. A stepper motor controls the motion of the cassette relative to an external magnetic field, which moves the magnetic beads through the reaction solutions automatically. Real-time fluorescence is used to measure the accumulation of dumbbells on the magnetic bead surface. Left-handed DNA dumbbells produce a distinct signal which reflects the level of non-specific amplification, acting as an internal control. The autoPiLOT assay detected as little as 5 fM target DNA, and was also successfully applied to the detection of S. mansoni DNA. The autoPiLOT design is a novel step forward in the development of a sensitive, user-friendly, low-resource, non-enzymatic diagnostic test.
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21
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Abstract
DNA amplification is a fundamental technique in molecular biology. The replication cycle reaction is a new method for amplification of large circular DNA having oriC sequences, which is a replication initiation site of the Escherichia coli chromosome. We here developed a replication cycle reaction-based method useful for amplification of various circular DNAs lacking oriC, even in the absence of any sequence information, via transposon-mediated oriC insertion to the circular DNA template. A 15-kb non-oriC plasmid was amplified from a very small amount of starting DNA (50 fg, 1 fM). The method was also applicable to GC-rich plasmid (69%) or large F-plasmid (230 kb). This method thus provides a powerful tool to amplify various environmental circular DNAs.
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22
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Barthet MM. Teaching molecular techniques at home: Molecular biology labs that can be performed anywhere and enable hands-on learning of restriction digestion/ligation and DNA amplification. Biochem Mol Biol Educ 2021; 49:598-604. [PMID: 33900019 DOI: 10.1002/bmb.21517] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
COVID 19 has changed about every aspect of life including how we teach in higher education. Laboratory experiments vital for learning hands-on techniques are limited due to social distancing requirements and increased numbers of distance-learning students. The solution to loss of hands-on activities has been to compensate with virtual laboratory modules. Although virtual labs are engaging and offer a simulated hands-on approach to teaching essential molecular techniques, these simulations do not replace hands-on experience. I designed two molecular biology laboratory exercises in response to the current teaching limitations that can be completed 'at-home' and enable low cost hands-on instruction of essential molecular techniques in any distance-learning environment including during the COVID 19 pandemic.
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Affiliation(s)
- Michelle M Barthet
- Department of Biology, Coastal Carolina University, Conway, South Carolina, USA
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23
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Abstract
Flow cytometric analysis and sorting of plant mitotic chromosomes has been mastered by only a few laboratories worldwide. Yet, it has been contributing significantly to progress in plant genetics, including the production of genome assemblies and the cloning of important genes. The dissection of complex genomes by flow sorting into the individual chromosomes that represent small parts of the genome reduces DNA sample complexity and streamlines projects relying on molecular and genomic techniques. Whereas flow cytometric analysis, that is, chromosome classification according to fluorescence and light scatter properties, is an integral part of any chromosome sorting project, it has rarely been used on its own due to lower resolution and sensitivity as compared to other cytogenetic methods. To perform chromosome analysis and sorting, commercially available electrostatic droplet sorters are suitable. However, in order to resolve and purify chromosomes of interest the instrument must offer high resolution of optical signals as well as stability during long runs. The challenge is thus not the instrumentation, but the adequate sample preparation. The sample must be a suspension of intact mitotic metaphase chromosomes and the protocol, which includes the induction of cell cycle synchrony, accumulation of dividing cells at metaphase, and release of undamaged chromosomes, is time consuming and laborious and needs to be performed very carefully. Moreover, in addition to fluorescent staining chromosomal DNA, the protocol may include specific labelling of DNA repeats to facilitate discrimination of particular chromosomes. This review introduces the applications of chromosome sorting in plants, and discusses in detail sample preparation, chromosome analysis and sorting to achieve the highest purity in flow-sorted fractions, and their suitability for downstream applications.
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Affiliation(s)
- Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Sergio Lucretti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
| | - István Molnár
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Petr Cápal
- Institute of Experimental Botany of the Czech Academy of SciencesCentre of the Region Haná for Biotechnological and Agricultural ResearchOlomoucCzech Republic
| | - Debora Giorgi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA)Division of Biotechnology and AgroindustryRomeItaly
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Boyle AG, Rankin SC, O'Shea K, Stefanovski D, Peng J, Song J, Bau HH. Detection of Streptococcus equi subsp. equi in guttural pouch lavage samples using a loop-mediated isothermal nucleic acid amplification microfluidic device. J Vet Intern Med 2021; 35:1597-1603. [PMID: 33728675 PMCID: PMC8163136 DOI: 10.1111/jvim.16105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 01/01/2023] Open
Abstract
Background Rapid point‐of‐care (POC) detection of Streptococcus equi subsp. equi (S. equi) would theoretically reduce the spread of strangles by identifying index and carrier horses. Hypothesis That the eqbE isothermal amplification (LAMP) assay, and the same eqbE LAMP assay tested in a microfluidic device format, are comparable to a triplex real‐time quantitative polymerase chain reaction (qPCR) assay that is commonly used in diagnostic labs. Samples Sixty‐eight guttural pouch lavage (GPL) specimens from horses recovering from strangles. Methods Guttural pouch lavage specimens were tested for S. equi retrospectively using the benchtop eqbE LAMP, the eqbE LAMP microfluidic device, and compared to the triplex qPCR, that detects 2 S. equi‐specific genes, eqbE and SEQ2190, as the reference standard using the receiver operating characteristic area under the curve (ROC). Results The 27/68 specimens were positive by benchtop eqbE LAMP, 31/64 by eqbE LAMP microfluidic device, and 12/67 by triplex qPCR. Using the triplex PCR as the reference, the benchtop eqbE LAMP showed excellent discrimination (ROC Area = 0.813, 95% confidence interval [CI] = 0.711‐0.915) as did the LAMP microfluidic device (ROC Area = 0.811, 95% CI = 0.529‐0.782). There was no significant difference between the benchtop LAMP and LAMP microfluidic device (ROC Area 0.813 ± 0.055 vs 0.811 ± 0.034, P = .97). Conclusions The eqbE LAMP microfluidic device detected S. equi in GPL specimens from convalescent horses. This assay shows potential for development as a POC device for rapid, sensitive, accurate, and cost‐efficient detection of S. equi.
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Affiliation(s)
- Ashley G Boyle
- Department of Clinical Studies-New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Shelley C Rankin
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen O'Shea
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Darko Stefanovski
- Department of Clinical Studies-New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Jing Peng
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jinzhao Song
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Haim H Bau
- Department of Mechanical Engineering and Applied Mechanics, School of Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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25
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Li H, Liu P, Gunawan R, Simeneh ZM, Liang C, Yao X, Yang M. Magnetothermal Miniature Reactors Based on Fe 3 O 4 Nanocube-Coated Liquid Marbles. Adv Healthc Mater 2021; 10:e2001658. [PMID: 33470539 DOI: 10.1002/adhm.202001658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/17/2020] [Indexed: 12/26/2022]
Abstract
Liquid marbles have recently attracted much interest in various scientific fields because of their isolated environment and robustness. However, conventional liquid marbles lack a reliable heating mechanism, which is critical in many potential applications. Here, the development of iron oxide (Fe3 O4 ) nanocube-coated liquid marbles (iNLMs), which can be homogeneously heated with an alternating magnetic field (AMF) to as high as 86 °C, is reported. Through tuning the power of the AMF, the iNLMs canbe heated to desired temperatures in controllable patterns. Furthermore, multicenter and selective heating is realized based on the unique magnetothermal properties of iNLMs. As heatable miniature reactors, the iNLMs are further demonstrated to facilitate the kinetic study of temperature-dependent chemical reactions. DNA amplification is successfully performed in liquid marbles, achieving a 25% superior amplification rate compared with that in a common thermal cycler. These results confirm the feasibility of coating liquid marbles with Fe3 O4 nanocubes to form delicate magnetothermal miniature reactors, which provides a reliable method of applying liquid marbles in areas such as biosensor technology, point-of-care testing, and theranostics.
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Affiliation(s)
- Hualin Li
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Peng Liu
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Renardi Gunawan
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Zemenu Mengistie Simeneh
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Chen Liang
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Xi Yao
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, 83 Tat Chee Ave, Kowloon Tong, Hong Kong SAR, P. R. China
- Key Laboratory of Biochip Technology, Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, P. R. China
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Zadesenets KS, Rubtsov NB. Regions enriched for DNA repeats in chromosomes of Macrostomum mirumnovem, a species with a recent Whole Genome Duplication. Vavilovskii Zhurnal Genet Selektsii 2020; 24:636-642. [PMID: 33659849 PMCID: PMC7716556 DOI: 10.18699/vj20.657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The free-living flatworm Macrostomum mirumnovem is a neopolyploid species whose genome underwent
a recent Whole Genome Duplication (WGD). In the result of chromosome fusions of the ancient haploid
chromosome set, large metacentric chromosomes were formed. In addition to three pairs of small metacentrics,
the current karyotype of M. mirumnovem contains two pairs of large metacentric chromosomes, MMI1 and MMI2.
The generation of microdissected DNA libraries enriched for DNA repeats followed by DNA probe preparation and
fluorescent in situ hybridization (FISH) were performed. The DNA probes obtained marked chromosome regions
enriched for different DNA repeats in the M. mirumnovem chromosomes. The size and localization of these regions
varied in different copies of large chromosomes. They varied even in homologous chromosomes, suggesting their
divergence due to genome re-diploidization after a WGD. Besides the newly formed chromosome regions enriched
for DNA repeats, B chromosomes were found in the karyotypes of the studied specimens of M. mirumnovem. These
B chromosomes varied in size and morphology. FISH with microdissected DNA probes revealed that some Bs had
a distinct DNA content. FISH could paint differently B chromosomes in different worms and even in the same sample.
B chromosomes could carry a bright specific fluorescent signal or could show no fluorescent signal at all. In latter
cases, the specific FISH signal could be absent even in the pericentromeric region of the B chromosome. Possible
mechanisms of B chromosome formation and their further evolution are discussed. The results obtained indicate
an important role that repetitive DNAs play in genome re-diploidization initiating a rapid differentiation of large
chromosome copies. Taking together, karyotype peculiarities (a high level of intraspecific karyotypic diversity associated
with chromosome number variation, structural chromosomal rearrangements, and the formation of new
regions enriched for DNA repeats) and some phenotypic features of M. mirumnovem (small body size, short lifecycle,
easy maintenance in the laboratory) make this species a perspective model in the studies of genomic and
karyotypic evolution in species passed through a recent WGD event.
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Affiliation(s)
- K S Zadesenets
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N B Rubtsov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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27
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Seo MJ, Yoo JC. Fully Automated Lab-On-A-Disc Platform for Loop-Mediated Isothermal Amplification Using Micro-Carbon-Activated Cell Lysis. Sensors (Basel) 2020; 20:E4746. [PMID: 32842600 DOI: 10.3390/s20174746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/17/2020] [Accepted: 08/20/2020] [Indexed: 11/17/2022]
Abstract
Fast and fully automated deoxyribonucleic acid (DNA) amplification methods are of interest in the research on lab-on-a-disc (LOD) platforms because of their full compatibility with the spin-column mechanism using centrifugal force. However, the standard procedures followed in DNA amplification require accurate noncontact temperature control as well as cell lysis at a low temperature to prevent damage to the LOD platform. This requirement makes it challenging to achieve full automation of DNA amplification on an LOD. In this paper, a fully automated LOD capable of performing cell lysis and amplification on a single compact disc of DNA samples is proposed. The proposed system uses micro-carbon to heat DNA samples without damaging the LOD as well as a noncontact heating system and an infrared camera sensor to remotely measure the real temperature of the amplification chamber. Compared with conventional DNA amplification systems, the proposed system has the advantage of full automation of the LOD platform. Experimental results demonstrated that the proposed system offers a stable heating method for DNA amplification and cell lysis.
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28
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Bush J, Singh S, Vargas M, Oktay E, Hu CH, Veneziano R. Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:E3386. [PMID: 32722650 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
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29
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Matsuo M, Hirata Y, Kurihara K, Toyota T, Miura T, Suzuki K, Sugawara T. Environment-Sensitive Intelligent Self-Reproducing Artificial Cell with a Modification-Active Lipo-Deoxyribozyme. Micromachines (Basel) 2020; 11:E606. [PMID: 32580457 DOI: 10.3390/mi11060606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/09/2020] [Accepted: 06/19/2020] [Indexed: 12/17/2022]
Abstract
As a supramolecular micromachine with information flow, a giant vesicle (GV)-based artificial cell that exhibits a linked proliferation between GV reproduction and internal DNA amplification has been explored in this study. The linked proliferation is controlled by a complex consisting of GV membrane-intruded DNA with acidic amphiphilic catalysts, working overall as a lipo-deoxyribozyme. Here, we investigated how a GV-based artificial cell containing this lipo-deoxyribozyme responds to diverse external and internal environments, changing its proliferative dynamics. We observed morphological changes (phenotypic expression) in GVs induced by the addition of membrane precursors with different intervals of addition (starvation periods). First, we focused on a new phenotype, the “multiple tubulated” form, which emerged after a long starvation period. Compared to other forms, the multiple tubulated form is characterized by a larger membrane surface with a heavily cationic charge. A second consideration is the effect of the chain length of encapsulated DNA on competitive proliferation. The competitive proliferation among three different species of artificial cells containing different lengths of DNA was investigated. The results clearly showed a distinct intervention in the proliferation dynamics of the artificial cells with each other. In this sense, our GV-based artificial cell can be regarded as an intelligent supramolecular machine responding to external and internal environments, providing a new concept for developing molecular machines and robotics.
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30
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López Zúñiga MÁ, Chueca N, de Salazar A, Fernández Caballero JA, Gutierrez Valencia A, Vinuesa García D, Omar Mohamed Balgahata M, Hidalgo Tenorio C, Lopez-Ruz MA, Garcia F. Genetic diversity of HIV in seminal plasma remains higher than in blood after short-term antiretroviral therapy. Sex Transm Infect 2020; 96:337-341. [PMID: 32245779 PMCID: PMC7402555 DOI: 10.1136/sextrans-2020-054439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 11/23/2022] Open
Abstract
Objective To provide insight on viral kinetics and genetic diversity of HIV in seminal plasma at baseline and 1 month after initiating antiretroviral therapy (ART). Patients and methods Blood and seminal samples from patients with newly diagnosed HIV were obtained before ART initiation (T0) and 1 month after ART initiation (T1). HIV env genetic diversity was studied using deep sequencing Nextera and V3 chemistry in a MiSeq Illumina platform. The number of viral quasispecies (5% cut-off) and Shannon Index were used to analyse diversity. Results Forty-seven ART-naive patients were recruited between September 2016 and November 2018. At enrolment, the number of quasispecies in blood (median 4 (IQR 2–5)) was lower than in the seminal compartment (median 6, (IQR 4–8)) (p<0.01); the Shannon Index was also higher (p<0.001) in the seminal compartment than in blood (1.77 vs 0.64). At T1, for the 13 patients with detectable HIV in both blood/seminal plasma, viral diversity remained higher (p=0.139) in seminal plasma (median 2 (IQR 1–4.5)) than in blood (median 1 (IQR 1–1.5)) Integrase inhibitors (INI)-based regimens achieved higher levels of undetectability and led more frequently to lower variability (p<0.001) than protease inhibitors (PI) or non-nucleoside reverse transcriptase inhibitors (NNRTI). Conclusion We provide here further evidence of a larger genetic diversity in seminal plasma, both at diagnosis and short term after ART initiation. Our results strengthen previous findings on HIV diversity in seminal plasma. In addition, INIs decrease variability more rapidly than PI and NNRTI in both blood and seminal plasma.
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Affiliation(s)
| | - Natalia Chueca
- Microbiology Department, San Cecilio University Hospital, Granada, Spain.,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
| | - Adolfo de Salazar
- Microbiology Department, San Cecilio University Hospital, Granada, Spain
| | | | | | | | | | | | - Miguel Angel Lopez-Ruz
- Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain.,Infectious Disease Service, University Hospital Virgen de las Nieves, Granada, Spain
| | - Federico Garcia
- Microbiology Department, San Cecilio University Hospital, Granada, Spain .,Instituto de Investigación Biosanitaria Ibs.Granada, Granada, Spain
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31
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Skowron PM, Krawczun N, Żebrowska J, Krefft D, Żołnierkiewicz O, Bielawa M, Jeżewska-Frąckowiak J, Janus Ł, Witkowska M, Palczewska M, Schumacher A, Wardowska A, Deptuła M, Czupryn A, Mucha P, Piotrowski A, Sachadyn P, Rodziewicz-Motowidło S, Pikuła M, Zylicz-Stachula A. Data regarding a new, vector-enzymatic DNA fragment amplification-expression technology for the construction of artificial, concatemeric DNA, RNA and proteins, as well as biological effects of selected polypeptides obtained using this method. Data Brief 2020; 28:105069. [PMID: 31956674 PMCID: PMC6956754 DOI: 10.1016/j.dib.2019.105069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 10/25/2022] Open
Abstract
Applications of bioactive peptides and polypeptides are emerging in areas such as drug development and drug delivery systems. These compounds are bioactive, biocompatible and represent a wide range of chemical properties, enabling further adjustments of obtained biomaterials. However, delivering large quantities of peptide derivatives is still challenging. Several methods have been developed for the production of concatemers - multiple copies of the desired protein segments. We have presented an efficient method for the production of peptides of desired length, expressed from concatemeric Open Reading Frame. The method employs specific amplification-expression DNA vectors. The main methodological approaches are described by Skowron et al., 2020 [1]. As an illustration of the demonstrated method's utility, an epitope from the S protein of Hepatitis B virus (HBV) was amplified. Additionally, peptides, showing potentially pro-regenerative properties, derived from the angiopoietin-related growth factor (AGF) were designed and amplified. Here we present a dataset including: (i) detailed protocols for the purification of HBV and AGF - derived polyepitopic protein concatemers, (ii) sequences of the designed primers, vectors and recombinant constructs, (iii) data on cytotoxicity, immunogenicity and stability of AGF-derived polypeptides.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Natalia Krawczun
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Joanna Żebrowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Olga Żołnierkiewicz
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | | | - Joanna Jeżewska-Frąckowiak
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Łukasz Janus
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
| | - Małgorzata Witkowska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Małgorzata Palczewska
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland
| | - Adriana Schumacher
- Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland.,Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland
| | - Anna Wardowska
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland.,Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Milena Deptuła
- Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Artur Czupryn
- Nencki Institute of Experimental Biology, Warsaw, 02-093, Poland
| | - Piotr Mucha
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdansk, 80-308, Poland
| | - Arkadiusz Piotrowski
- Department of Biology and Pharmaceutical Botany, Faculty of Pharmacy, Medical University of Gdansk, 80-416, Poland.,International Research Agenda - 3P Medicine Lab, Medical University of Gdansk, 80-416, Poland
| | - Paweł Sachadyn
- Laboratory for Regenerative Biotechnology, Faculty of Chemistry, Gdansk University of Technology, Gdansk, 80-233, Poland
| | | | - Michał Pikuła
- Department of Clinical Immunology and Transplantology, Faculty of Medicine, Medical University of Gdansk, 80-210, Poland.,Laboratory of Tissue Engineering and Regenerative Medicine, Department of Embryology, Faculty of Medicine, Medical University of Gdansk, Gdansk, 80-211, Poland
| | - Agnieszka Zylicz-Stachula
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Gdansk, 80-308, Poland.,BioVentures Institute Ltd., Poznan, 60-141, Poland
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Rubinfien J, Atabay KD, Nichols NM, Tanner NA, Pezza JA, Gray MM, Wagner BM, Poppin JN, Aken JT, Gleason EJ, Foley KD, Copeland DS, Kraves S, Alvarez Saavedra E. Nucleic acid detection aboard the International Space Station by colorimetric loop-mediated isothermal amplification (LAMP). FASEB Bioadv 2020; 2:160-165. [PMID: 32161905 PMCID: PMC7059625 DOI: 10.1096/fba.2019-00088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 10/30/2019] [Accepted: 12/30/2019] [Indexed: 12/22/2022] Open
Abstract
Human spaceflight endeavors present an opportunity to expand our presence beyond Earth. To this end, it is crucial to understand and diagnose effects of long‐term space travel on the human body. Developing tools for targeted, on‐site detection of specific DNA sequences will allow us to establish research and diagnostics platforms that will benefit space programs. We describe a simple DNA diagnostic method that utilizes colorimetric loop‐mediated isothermal amplification (LAMP) to enable detection of a repetitive telomeric DNA sequence in as little as 30 minutes. A proof of concept assay for this method was carried out using existing hardware on the International Space Station and the results were read instantly by an astronaut through a simple color change of the reaction mixture. LAMP offers a novel platform for on‐orbit DNA‐based diagnostics that can be deployed on the International Space Station and to the broader benefit of space programs.
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Affiliation(s)
| | - Kutay D Atabay
- Whitehead Institute for Biomedical Research Massachusetts Institute of Technology Cambridge MA USA
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Chen ZC, Chang TL, Li CH, Su KW, Liu CC. Thermally stable and uniform DNA amplification with picosecond laser ablated graphene rapid thermal cycling device. Biosens Bioelectron 2019; 146:111581. [PMID: 31629228 PMCID: PMC7126615 DOI: 10.1016/j.bios.2019.111581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/02/2019] [Accepted: 08/08/2019] [Indexed: 01/02/2023]
Abstract
Rapid thermal cycling (RTC) in an on-chip device can perform DNA amplification in vitro through precise thermal control at each step of the polymerase chain reaction (PCR). This study reports a straightforward fabrication technique for patterning an on-chip graphene-based device with hole arrays, in which the mechanism of surface structures can achieve stable and uniform thermal control for the amplification of DNA fragments. A thin-film based PCR device was fabricated using picosecond laser (PS-laser) ablation of the multilayer graphene (MLG). Under the optimal fluence of 4.72 J/cm2 with a pulse overlap of 66%, the MLG can be patterned with arrays of 250 μm2 hole surface structures. A 354-bp DNA fragment of VP1, an effective marker for diagnosing the BK virus, was amplified on an on-chip device in less than 60 min. A thin-film electrode with the aforementioned MLG as the heater was demonstrated to significantly enhance temperature stability for each stage of the thermal cycle. The temperature control of the heater was performed by means of a developed programmable PCR apparatus. Our results demonstrated that the proposed integration of a graphene-based device and a laser-pulse ablation process to form a thin-film PCR device has cost benefits in a small-volume reagent and holds great promise for practical medical use of DNA amplification.
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Affiliation(s)
- Zhao-Chi Chen
- Department of Mechatronic Engineering, National Taiwan Normal University, Taipei, Taiwan, ROC
| | - Tien-Li Chang
- Department of Mechatronic Engineering, National Taiwan Normal University, Taipei, Taiwan, ROC.
| | - Ching-Hao Li
- Department of Physiology, School of Medicine, Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan, ROC
| | - Kai-Wen Su
- Integrated Science, University of British Columbia, Columbia, Canada
| | - Cheng-Che Liu
- Graduate Institute of Physiology, National Defense Medical Center, Taipei, Taiwan, ROC.
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Wu Q, Zhang Y, Yang Q, Yuan N, Zhang W. Review of Electrochemical DNA Biosensors for Detecting Food Borne Pathogens. Sensors (Basel) 2019; 19:E4916. [PMID: 31718098 DOI: 10.3390/s19224916] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022]
Abstract
The vital importance of rapid and accurate detection of food borne pathogens has driven the development of biosensor to prevent food borne illness outbreaks. Electrochemical DNA biosensors offer such merits as rapid response, high sensitivity, low cost, and ease of use. This review covers the following three aspects: food borne pathogens and conventional detection methods, the design and fabrication of electrochemical DNA biosensors and several techniques for improving sensitivity of biosensors. We highlight the main bioreceptors and immobilizing methods on sensing interface, electrochemical techniques, electrochemical indicators, nanotechnology, and nucleic acid-based amplification. Finally, in view of the existing shortcomings of electrochemical DNA biosensors in the field of food borne pathogen detection, we also predict and prospect future research focuses from the following five aspects: specific bioreceptors (improving specificity), nanomaterials (enhancing sensitivity), microfluidic chip technology (realizing automate operation), paper-based biosensors (reducing detection cost), and smartphones or other mobile devices (simplifying signal reading devices).
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Abstract
Isothermal DNA amplification reactions are a prevalent tool with many applications, ranging from analyte detection to DNA circuits. Exponential amplification reaction (EXPAR) is a popular isothermal DNA amplification method that exponentially amplifies short DNA oligonucleotides. A recent modification of this technique using an energetically stable looped template with palindromic binding regions demonstrated unexpected biphasic amplification and much higher DNA yield than EXPAR. This ultrasensitive DNA amplification reaction (UDAR) shows high-gain, switch-like DNA output from low concentrations of DNA input. Here we present the first mathematical model of UDAR based on four reaction mechanisms and show the model can reproduce the experimentally observed biphasic behaviour. Furthermore, we show that three of these mechanisms are necessary to reproduce biphasic experimental results. The reaction mechanisms are (i) positively cooperative multistep binding spurred by two trigger binding sites on the template; (ii) gradual template deactivation; (iii) recycling of deactivated templates into active templates; and (iv) polymerase sequestration. These mechanisms can potentially illuminate the behaviour of EXPAR as well as other nucleic acid amplification reactions.
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Affiliation(s)
- Danielle Ciesielski
- 1 Department of Mathematical Sciences, Montana State University , Bozeman, MT 59715 , USA
| | - Burcu Özay
- 2 Department of Chemical and Biological Engineering, Montana State University , Bozeman, MT 59715 , USA
| | - Stephanie McCalla
- 2 Department of Chemical and Biological Engineering, Montana State University , Bozeman, MT 59715 , USA
| | - Tomas Gedeon
- 1 Department of Mathematical Sciences, Montana State University , Bozeman, MT 59715 , USA
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Cong H, Loo J, Chen J, Wang Y, Kong SK, Ho HP. Target trapping and in situ single-cell genetic marker detection with a focused optical beam. Biosens Bioelectron 2019; 133:236-242. [PMID: 30953882 DOI: 10.1016/j.bios.2019.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/04/2019] [Accepted: 02/12/2019] [Indexed: 01/01/2023]
Abstract
Optical trapping of single particles or cells with the capability of in situ bio-sensing or genetic profiling opens the possibility of rapid screening of biological specimens. However, common optical tweezers suffer from the lack of long-range forces. Consequently, their application areas are predominantly limited to target manipulation instead of biological diagnostics. To solve this problem, we herein report an all-in-one approach by combining optical forces and convective drag forces generated through localized optothermal effect for long-range target manipulation. The device consists of a 2D array of gold coated polydimethylsiloxane (PDMS) micro-wells, which are immersed by colloidal particles or cell solution. Upon excitation of a 785-nm laser, the hydrodynamic convective force and optical forces will drag the targets of interest into their designated micro-wells. Moreover, the plasmonic thermal dissipation provides a constant temperature environment for following cell analysis procedures of cell isolation, lysis and isothermal nucleic acid amplification for the detection of genetic markers. With the merits of fabrication simplicity, short sample-to-answer cycle time and the compatibility with optical microscopes, the reported technique offers an attractive and highly versatile approach for on-site single cell analysis systems.
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Affiliation(s)
- Hengji Cong
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacky Loo
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China; Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jiajie Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
| | - Yuye Wang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Siu-Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China.
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Vidic J, Vizzini P, Manzano M, Kavanaugh D, Ramarao N, Zivkovic M, Radonic V, Knezevic N, Giouroudi I, Gadjanski I. Point-of-Need DNA Testing for Detection of Foodborne Pathogenic Bacteria. Sensors (Basel) 2019; 19:E1100. [PMID: 30836707 PMCID: PMC6427207 DOI: 10.3390/s19051100] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Foodborne pathogenic bacteria present a crucial food safety issue. Conventional diagnostic methods are time-consuming and can be only performed on previously produced food. The advancing field of point-of-need diagnostic devices integrating molecular methods, biosensors, microfluidics, and nanomaterials offers new avenues for swift, low-cost detection of pathogens with high sensitivity and specificity. These analyses and screening of food items can be performed during all phases of production. This review presents major developments achieved in recent years in point-of-need diagnostics in land-based sector and sheds light on current challenges in achieving wider acceptance of portable devices in the food industry. Particular emphasis is placed on methods for testing nucleic acids, protocols for portable nucleic acid extraction and amplification, as well as on the means for low-cost detection and read-out signal amplification.
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Affiliation(s)
- Jasmina Vidic
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Priya Vizzini
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università di Udine, 33100 Udine, Italy.
| | - Devon Kavanaugh
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Milica Zivkovic
- Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, 11000 Belgrade, Serbia.
| | - Vasa Radonic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Nikola Knezevic
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ioanna Giouroudi
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
| | - Ivana Gadjanski
- BioSense-Research and Development Institute for Information Technologies in Biosystems, University of Novi Sad, 21000 Novi Sad, Serbia.
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Abstract
Introduction In this fast era of numerous unwanted disasters and because of the severely devastated and degenerated body remains, personal identification of unknown remains has become the most difficult and challenging task. In such instances, dental pulp plays a vital role in identification through deoxyribonucleic acid (DNA). Aim The aim of the study is to determine sex from tooth pulp tissues by DNA analysis using polymerase chain reaction amplification method under different environmental conditions. Materials and Methods The human extracted teeth were exposed to different conditions such as heat, soil, and open environment. The DNA was extracted from all these teeth including freshly extracted teeth, then quantified, and further amplified with male and female primers. Results Quantity of DNA content achieved ranged from 5.21 to 62.87 ng/μl. The accuracy in determining sex from pulp DNA ranged from 92% to 100% in the study groups, except from the teeth exposed to uncontrolled heat, as the pulp tissue was burnt completely. The intergroup analysis was statistically highly significant (P < 0.001). Gender determination using the quantity of DNA was found to be nonsignificant (P > 0.05). Conclusion The dental pulp is the reliable source for sex determination in the humid or dry environment compared to uncontrolled heat.
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Affiliation(s)
- Ruchi Kishor Pawar
- Department of Oral Medicine and Maxillofacial Radiology, K. M. Shah Dental College and Hospital, Sumandeep Vidyapeeth University, Vadodara, Gujarat, India
| | - Chandramani B More
- Department of Oral Medicine and Maxillofacial Radiology, K. M. Shah Dental College and Hospital, Sumandeep Vidyapeeth University, Vadodara, Gujarat, India
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Wang G, Wang H, Cao S, Xiang W, Li T, Yang M. Electrochemical determination of the activity and inhibition of telomerase based on the interaction of DNA with molybdate. Mikrochim Acta 2019; 186:96. [PMID: 30631950 DOI: 10.1007/s00604-018-3223-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/29/2018] [Indexed: 01/19/2023]
Abstract
An ultrasensitive electrochemical sensor is described for the determination of the activity of telomerase. It is based on a DNA-generated current that is due to the reaction of the phosphate groups on DNA with molybdate to form a redox-active molybdophosphate. A telomerase substrate primer was first immobilized on a gold electrode. In the presence of telomerase and deoxyribonucleoside triphosphates (dNTPs), the primer can be extended with repetitive nucleotide sequences (TTAGGG). The subsequent reaction of the sensor with molybdate results in the enhancement of electrochemical current intensity due to an increased amount of nucleotides on the electrode. Sensitivity can be further improved by introducing a hairpin probe that partially hybridizes with the repetitive TTAGGG sequence and further enhances the amount of DNA on the electrode. The biosensor, best operated at 0.2 V (vs. Ag/AgCl) shows a linear response to telomerase activity from 1×102 to 107 Hela cells mL-1. The assay was applied to the detection of telomerase activity in HeLa cancer cells treated with the anticancer drug epigallocatechin gallate, and the results indicate that it holds great potential in anticancer drug screening. Graphical abstract Schematic presentation of an ultrasensitive electrochemical sensor for the determination of telomerase activity based on DNA generated electrochemical current. dNTPs in the scheme represents deoxyribonucleoside triphosphates.
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40
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Leung V, Brooks M, Emerson S, Ali M, Filipe CDM. Ready-to-use thermally stable mastermix pills for molecular biology applications. Biotechnol Prog 2018; 35:e2764. [PMID: 30536873 DOI: 10.1002/btpr.2764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/14/2018] [Accepted: 12/06/2018] [Indexed: 11/12/2022]
Abstract
Rolling circle amplification (RCA), polymerase chain reaction (PCR), and loop-mediated isothermal amplification (LAMP), are powerful tools that can be used for gene manipulation, pathogen detection, and infectious disease diagnostics. However, these techniques require trained personnel, as the pipetting steps involved can lead to contamination and, consequently, erroneous results. Furthermore, many of the reagents used in molecular biology are thermally labile and must be kept within a cold-chain. In this article, we present a simple and cost-effective method that allows molecular biology reagents to be thermally stabilized into ready-to-use mastermixes via drying in pullulan and trehalose films. Our experimental results demonstrate that this method is capable of preserving the activity of RCA, PCR, LAMP, ligase, polynucleotide kinase, and Klenow fragment mastermixes for at least 3 months at ambient conditions. Thus, stabilizing reagents via drying in pullulan and trehalose film may allow for a drastic reduction in the number of pipetting steps and the elimination of the need for a cold chain. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2764, 2019.
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Affiliation(s)
- Vincent Leung
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Meredith Brooks
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Sophia Emerson
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Monsur Ali
- Biointerfaces Inst., McMaster University, Hamilton, L8S 4L7, Ontario, Canada
| | - Carlos D M Filipe
- Dept. of Chemical Engineering, 1280 Main Street West, McMaster University, Hamilton, L8S 4L7, Ontario, Canada
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Hasebe T, Narita K, Hidaka S, Su'etsugu M. Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction. Life (Basel) 2018; 8:life8040043. [PMID: 30257439 PMCID: PMC6315707 DOI: 10.3390/life8040043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/22/2018] [Accepted: 09/23/2018] [Indexed: 11/16/2022] Open
Abstract
Propagation of genetic information is a fundamental prerequisite for living cells. We recently developed the replication cycle reaction (RCR), an in vitro reaction for circular DNA propagation, by reconstitution of the replication cycle of the Escherichia coli chromosome. In RCR, two replication forks proceed bidirectionally from the replication origin, oriC, and meet at a region opposite oriC, yielding two copies of circular DNA. Although RCR essentially propagates supercoiled monomers, concatemer byproducts are also produced due to inefficient termination of the replication fork progression. Here, we examined the effect of the Tus-ter replication fork trap in RCR. Unexpectedly, when the fork traps were placed opposite oriC, mimicking their arrangement on the chromosome, the propagation of circular DNA was inhibited. On the other hand, fork traps flanking oriC allowed efficient propagation of circular DNA and repressed concatemer production. These findings suggest that collision of the two convergence forks through the fork trap is detrimental to repetition of the replication cycle. We further demonstrate that this detrimental effect was rescued by the UvrD helicase. These results provide insights into the way in which circular DNA monomers replicate repetitively without generating concatemers.
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Affiliation(s)
- Tomonori Hasebe
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Kouhei Narita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Shiomi Hidaka
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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42
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Mitchell SM, Rand KN, Xu ZZ, Ho T, Brown GS, Ross JP, Molloy PL. Helper-Dependent Chain Reaction (HDCR) for Selective Amplification of Methylated DNA Sequences. Methods Mol Biol 2018; 1708:587-601. [PMID: 29224165 DOI: 10.1007/978-1-4939-7481-8_30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Over the last few years a number of restriction enzymes that cut DNA only if cytosines within their recognition sequences are methylated have been characterized and become commercially available. Cleavage with these enzymes to release DNA fragments in a methylation-dependent manner can be combined with a novel method of amplification, Helper Dependent Chain Reaction (HDCR), to selectively amplify these fragments. HDCR uses "Helper" oligonucleotides as templates for extension of the free 3' end of target fragments to incorporate tag sequences at the ends of fragments. These tag sequences are then used for priming of amplification of target fragments. Modifications to the amplification primers (Drivers) and the Helpers ensure that there is selection for the sequences within target fragments with each cycle of amplification. The combination of methylation-dependent enzymes and HDCR allows the sensitive and selective amplification of methylated DNA sequences without the need for bisulfite treatment.
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Affiliation(s)
- Susan M Mitchell
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Keith N Rand
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Zheng-Zhou Xu
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Thu Ho
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Glenn S Brown
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Jason P Ross
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia
| | - Peter L Molloy
- CSIRO Food and Nutrition Flagship, PO Box 52, North Ryde, NSW, 1670, Australia.
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Lomidze L, Williford TH, Musier-Forsyth K, Kankia B. Isothermal amplification of long DNA segments by quadruplex priming amplification. Anal Methods 2018; 10:2972-2979. [PMID: 30505353 PMCID: PMC6261523 DOI: 10.1039/c8ay00843d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amplification of long DNA segments with the highest possible specificity and lowest bias is one of the main goals of modern genomics. Quadruplex priming amplification (QPA) is a single-primer isothermal method, which employs the free energy of quadruplex structures as the driving force for DNA amplification without any extra reaction components. As a result, QPA represents one of the simplest isothermal assays and was previously shown to be suitable for amplification of relatively short DNA sequences. The current study reveals that single-primer QPA can be used for both exponential and linear amplification of relatively long DNA segments (>100 nt), and switching between these modes can be accomplished by simple re-design of the primer used. While exponential amplification resulted in production of some undesired higher molecular weight species, linear QPA demonstrated highly specific amplification of the target molecules without any side products.
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Affiliation(s)
- Levan Lomidze
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
| | - Tyler H. Williford
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA
| | - Besik Kankia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA
- Institute of Biophysics, Ilia State University, Tbilisi 0162, Republic of Georgia
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Kant K, Shahbazi MA, Dave VP, Ngo TA, Chidambara VA, Than LQ, Bang DD, Wolff A. Microfluidic devices for sample preparation and rapid detection of foodborne pathogens. Biotechnol Adv 2018; 36:1003-24. [PMID: 29534915 DOI: 10.1016/j.biotechadv.2018.03.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rapid detection of foodborne pathogens at an early stage is imperative for preventing the outbreak of foodborne diseases, known as serious threats to human health. Conventional bacterial culturing methods for foodborne pathogen detection are time consuming, laborious, and with poor pathogen diagnosis competences. This has prompted researchers to call the current status of detection approaches into question and leverage new technologies for superior pathogen sensing outcomes. Novel strategies mainly rely on incorporating all the steps from sample preparation to detection in miniaturized devices for online monitoring of pathogens with high accuracy and sensitivity in a time-saving and cost effective manner. Lab on chip is a blooming area in diagnosis, which exploits different mechanical and biological techniques to detect very low concentrations of pathogens in food samples. This is achieved through streamlining the sample handling and concentrating procedures, which will subsequently reduce human errors and enhance the accuracy of the sensing methods. Integration of sample preparation techniques into these devices can effectively minimize the impact of complex food matrix on pathogen diagnosis and improve the limit of detections. Integration of pathogen capturing bio-receptors on microfluidic devices is a crucial step, which can facilitate recognition abilities in harsh chemical and physical conditions, offering a great commercial benefit to the food-manufacturing sector. This article reviews recent advances in current state-of-the-art of sample preparation and concentration from food matrices with focus on bacterial capturing methods and sensing technologies, along with their advantages and limitations when integrated into microfluidic devices for online rapid detection of pathogens in foods and food production line.
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Maszczak-Seneczko D, Sosicka P, Olczak T, Olczak M. In Situ Proximity Ligation Assay (PLA) Analysis of Protein Complexes Formed Between Golgi-Resident, Glycosylation-Related Transporters and Transferases in Adherent Mammalian Cell Cultures. Methods Mol Biol 2016; 1496:133-43. [PMID: 27632007 DOI: 10.1007/978-1-4939-6463-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In situ proximity ligation assay (PLA) is a novel, revolutionary technique that can be employed to visualize protein complexes in fixed cells and tissues. This approach enables demonstration of close (i.e., up to 40 nm) proximity between any two proteins of interest that can be detected using a pair of specific antibodies that have been raised in distinct species. Primary antibodies bound to the target proteins are subsequently recognized by two PLA probes, i.e., secondary antibodies conjugated with oligonucleotides that anneal when brought into close proximity in the presence of two connector oligonucleotides and a DNA ligase forming a circular DNA molecule. In the next step, the resulting circular DNA is amplified by a rolling circle polymerase. Finally, fluorescent oligonucleotide probes hybridize to complementary fragments of the amplified DNA molecule, forming a typical, spot-like pattern of PLA signal that reflects subcellular localization of protein complexes. Here we describe the use of in situ PLA in adherent cultures of mammalian cells in order to visualize interactions between Golgi-resident, functionally related glycosyltransferases and nucleotide sugar transporters relevant to N-glycan biosynthesis.
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Robertson JM, Anders DL, Basalyga F, Millar J, Slack DP, Bever R. Effect of Sterilants on Amplification and Detection of Target DNA from Bacillus cereus Spores. J Forensic Sci 2017; 63:699-707. [PMID: 29139119 DOI: 10.1111/1556-4029.13653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 11/28/2022]
Abstract
To conceal criminal activity of a bioterrorist or agroterrorist, the site of pathogen generation is often treated with sterilants to kill the organisms and remove evidence. As dead organisms cannot be analyzed by culture, this study examined whether DNA from sterilant-treated Bacillus cereus spores was viable for amplification. The spores were exposed to five common sterilants: bleach, Sterilox®, oxidizer foam (L-Gel), a peroxyacid (Actril®), and formaldehyde vapor. The spores were inoculated on typical surfaces found in offices and laboratories to test for environmental effects. It was found that the surface influenced the efficiency of recovery of the organisms. The DNA isolated from the recovered spores was successfully detected using RT-qPCR for all treatments except for formaldehyde, by amplifying the phosphatidylinositol phospholipase C and sphingomyelinase genes. The results demonstrated that evidence from sites treated with sterilants can still provide information on the uncultured organism, using DNA amplification.
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Affiliation(s)
- James M Robertson
- Counterterrorism and Forensic Science Research Unit, FBI Laboratory, Quantico, VA, 22135
| | - Douglas L Anders
- Scientific Response Analysis Unit, FBI Laboratory, Quantico, VA, 22135
| | | | - Julie Millar
- Bode Cellmark Forensics, Inc., Lorton, VA, 22079
| | | | - Robert Bever
- Bode Cellmark Forensics, Inc., Lorton, VA, 22079
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Gaydos CA, Klausner JD, Pai NP, Kelly H, Coltart C, Peeling RW. Rapid and point-of-care tests for the diagnosis of Trichomonas vaginalis in women and men. Sex Transm Infect 2017; 93:S31-S35. [PMID: 28684611 DOI: 10.1136/sextrans-2016-053063] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/24/2017] [Accepted: 04/29/2017] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Trichomonasvaginalis (TV) is a highly prevalent parasitic infection worldwide. It is associated with many adverse reproductive health outcomes. Many infections are asymptomatic and syndromic management leads to underdetection of TV. Traditional methods of TV detection such as wet preparation are insensitive. New rapid, point-of-care (POC) tests can enhance the diagnosis of trichomoniasis. METHODS The authors reviewed the literature and discuss older POC tests for TV detection, as well as the OSOM lateral flow test, the AmpliVue test, the Solana test and the GeneXpert test as well as the limitations of wet preparation and culture for detection of TV. RESULTS The OSOM test is easy to perform, compared with other POC tests, and is Clinical Laboratory Improvement Amendments (CLIA)-waived, equipment-free, has sensitivities of 83%-86% compared with nucleic acid amplification tests (NAATs) and can be performed in 15 min. The AmpliVue and the Solana tests are not CLIA waived and require small pieces of equipment. They are molecular amplified assays and can be completed in <1 hour. AmpliVue demonstrated a sensitivity for vaginal swabs of 100% compared with wet preparation/culture and 90.7% compared with NAATs. Solana demonstrated a sensitivity of 98.6%-100% for vaginal swabs and 92.9%-98% for female urines, compared with wet preparation/culture. Compared with other NAATs, the sensitivity for Solana was 89.7% for swabs and 100% for urine. The GeneXpert TV test for women and men is a moderately complex test, requires a small platform and can be performed in <1 hour. The sensitivity compared with wet preparation/culture for self-collected vaginal swabs was 96.4%, 98.9% for endocervical specimens and 98.4% for female urine. For men, sensitivity for urines was excellent (97.2%). The specificity for all assays was excellent. CONCLUSIONS Several rapid POC tests have the potential to rapidly diagnose trichomoniasis in women and one is available for detection of TV in men.
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Affiliation(s)
- Charlotte A Gaydos
- Division of Infectious Diseases, Medicine Baltimore, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey D Klausner
- Division of Infectious Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Nitika Pant Pai
- Department of Epidemiology, McGill University, Montreal, Canada
| | - Helen Kelly
- London School of Hygiene & Tropical Medicine, London, UK
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Li C, Yu Z, Fu Y, Pang Y, Huang Y. Single-Cell-Based Platform for Copy Number Variation Profiling through Digital Counting of Amplified Genomic DNA Fragments. ACS Appl Mater Interfaces 2017; 9:13958-13964. [PMID: 28337907 DOI: 10.1021/acsami.7b03146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We develop a novel single-cell-based platform through digital counting of amplified genomic DNA fragments, named multifraction amplification (mfA), to detect the copy number variations (CNVs) in a single cell. Amplification is required to acquire genomic information from a single cell, while introducing unavoidable bias. Unlike prevalent methods that directly infer CNV profiles from the pattern of sequencing depth, our mfA platform denatures and separates the DNA molecules from a single cell into multiple fractions of a reaction mix before amplification. By examining the sequencing result of each fraction for a specific fragment and applying a segment-merge maximum likelihood algorithm to the calculation of copy number, we digitize the sequencing-depth-based CNV identification and thus provide a method that is less sensitive to the amplification bias. In this paper, we demonstrate a mfA platform through multiple displacement amplification (MDA) chemistry. When performing the mfA platform, the noise of MDA is reduced; therefore, the resolution of single-cell CNV identification can be improved to 100 kb. We can also determine the genomic region free of allelic drop-out with mfA platform, which is impossible for conventional single-cell amplification methods.
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Affiliation(s)
- Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - Zhilong Yu
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - Yusi Fu
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University , Beijing 100871, China
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Azeroglu B, Leach DRF. RecG controls DNA amplification at double-strand breaks and arrested replication forks. FEBS Lett 2017; 591:1101-1113. [PMID: 28155219 PMCID: PMC5412681 DOI: 10.1002/1873-3468.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/16/2022]
Abstract
DNA amplification is a powerful mutational mechanism that is a hallmark of cancer and drug resistance. It is therefore important to understand the fundamental pathways that cells employ to avoid over‐replicating sections of their genomes. Recent studies demonstrate that, in the absence of RecG, DNA amplification is observed at sites of DNA double‐strand break repair (DSBR) and of DNA replication arrest that are processed to generate double‐strand ends. RecG also plays a role in stabilising joint molecules formed during DSBR. We propose that RecG prevents a previously unrecognised mechanism of DNA amplification that we call reverse‐restart, which generates DNA double‐strand ends from incorrect loading of the replicative helicase at D‐loops formed by recombination, and at arrested replication forks.
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Affiliation(s)
- Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
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Pîrlea S, Puiu M, Răducan A, Oancea D. Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples. Int J Legal Med 2016; 131:323-331. [PMID: 27595149 DOI: 10.1007/s00414-016-1443-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/23/2016] [Indexed: 11/25/2022]
Abstract
In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.
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Affiliation(s)
- Sorina Pîrlea
- National Forensic Science Institute, Şoseaua Ştefan cel Mare 13-15, sect. 2, 020123, Bucharest, Romania
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Mihaela Puiu
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
| | - Adina Răducan
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania.
| | - Dumitru Oancea
- Department of Physical Chemistry, Faculty of Chemistry, University of Bucharest, Bd. Regina Elisabeta, Nr. 4-12, Bucharest, 030018, Romania
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